cBioPortal validation report

Study directory:
/datahub/serra_pnf_ntap_2023

For details, please see the documentation on file formats supported by cBioPortal

cBioPortal version 5.4.7-dirty-SNAPSHOT

Validation status: Failed
Line Number Column Number Message Value Encountered
Debug – – Requesting info from portal at 'http://cbioportal.org' –
Debug – – Requesting cancer-types from portal at 'http://cbioportal.org' –
Debug – – Requesting genes from portal at 'http://cbioportal.org' –
Debug – – Requesting genesets from portal at 'http://cbioportal.org' –
Debug – – Requesting genesets_version from portal at 'http://cbioportal.org' –
Debug – – Requesting gene-panels from portal at 'http://cbioportal.org' –
Error – – Cancer type of study is neither known to the portal nor defined in a cancer_type file pnf
Info – – No directory named 'case_lists' found, so assuming no custom case lists. –
Info – – Validation complete –
Line Number Column Number Message Value Encountered
Debug – – Starting validation of file –
Warning – – Columns OS_MONTHS and/or OS_STATUS not found. Overall survival analysis feature will not be available for this study. –
Warning – – Columns DFS_MONTHS and/or DFS_STATUS not found. Disease free analysis feature will not be available for this study. –
Info – – Validation of file complete –
Info – – Read 9 lines. Lines with warning: 0. Lines with error: 0 –
Line Number Column Number Message Value Encountered
Debug – – Starting validation of file –
Info – – Validation of file complete –
Info – – Read 32 lines. Lines with warning: 0. Lines with error: 0 –
Line Number Column Number Message Value Encountered
Debug – – Starting validation of file –
Warning 1 – The recommended column Entrez_Gene_Id was not found. Using Hugo_Symbol for all gene parsing. –
Warning 6, 91, 174… – Gene symbol not known to the cBioPortal instance. This record will not be loaded. C1ORF112, FAM214B, KIAA0100… See all 23794 values
Warning 26, 5510, 5512… – Duplicate line for a previously listed feature/gene, this line will be ignored. 4267 (already defined on line 25), 6845 (already defined on line 5509), 3581 (already defined on line 5511)… See all 128 values
Warning 19371, 51127, 52334… – Hugo Symbol is not in gene or alias table and starts with a number. This can be caused by unintentional gene conversion in Excel. 7SK, 5_8S_RRNA, 5S_RRNA See all 26 values
Info – – Validation of file complete –
Info – – Read 61599 lines. Lines with warning: 23923. Lines with error: 0 –
Line Number Column Number Message Value Encountered
Debug – – Starting validation of file –
Warning 1 – The recommended column Entrez_Gene_Id was not found. Using Hugo_Symbol for all gene parsing. –
Warning 6, 91, 174… – Gene symbol not known to the cBioPortal instance. This record will not be loaded. C1ORF112, FAM214B, KIAA0100… See all 23794 values
Warning 26, 5510, 5512… – Duplicate line for a previously listed feature/gene, this line will be ignored. 4267 (already defined on line 25), 6845 (already defined on line 5509), 3581 (already defined on line 5511)… See all 128 values
Warning 19371, 51127, 52334… – Hugo Symbol is not in gene or alias table and starts with a number. This can be caused by unintentional gene conversion in Excel. 7SK, 5_8S_RRNA, 5S_RRNA See all 26 values
Info – – Validation of file complete –
Info – – Read 61599 lines. Lines with warning: 23923. Lines with error: 0 –
Line Number Column Number Message Value Encountered
Debug – – Starting validation of meta file –
Info – – Validation of meta file complete –
Line Number Column Number Message Value Encountered
Debug – – Starting validation of meta file –
Info – – Validation of meta file complete –
Line Number Column Number Message Value Encountered
Debug – – Starting validation of meta file –
Info – – Validation of meta file complete –
Line Number Column Number Message Value Encountered
Debug – – Starting validation of meta file –
Info – – Validation of meta file complete –
Line Number Column Number Message Value Encountered
Debug – – Starting validation of meta file –
Info – – Validation of meta file complete –
Info – – No reference genome specified -- using default (hg19) –

Legend

Click on a filename below to see a table of messages about the data in the file. The colors in the tables have the following meanings:

Error Error: cBioPortal will not know how to load this, please revise or remove
Warning Warning: possible cause of confusion, please check whether this is intended
Info Info: this looks good, no action required
Debug Verbose output: details on the progress of the validation script